Meet the Microbiologist

Moon Nahm, M.D., professor emeritus at UAB Department of Medicine and Director of the World Health Organization's Pneumococcal Serology Reference Laboratory at UAB, discusses his career in pneumococcal immunology. From uncovering the WU2 reference strain and other hidden serotypes to pioneering Multiplexed Opsono-Phagocytosis Assay (MOPA) to measure the functional activity of anti-pneumococcal antibodies, Nahm's contributions have facilitated development of advanced vaccines with broader protection and accessibility. Links for This Episode UAB Spotlight on Moon Nahm. Discovery and Characterization of Pneumococcal Serogroup 36 Capsule Subtypes, Serotypes 36A and 36B. Journal of Clinical Microbiology paper, March 27, 2003. A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cpsFragment from an Oral Streptococcus. mBio, May 19, 2020. 50 years—and change. WashU Magazine. MTM Listener Survey

From leading R&D at a biotech startup company to conducting environmental monitoring for NASA, Veronica Garcia, Ph.D., Scientific Director of the ASM Applied and Environmental Microbiology unit shares how experiences throughout her career have informed her appreciation for microbes and their real-world applications. She also discusses how the ASM AEM unit will support scientists around the globe by fostering collaboration and advocating for scientific advancements in areas like climate change, water systems and food production. Ashley's Biggest Takeaways Prior to her role as Scientific Director for ASM Applied and Environmental Microbiology unit, Garcia was Senior Director of R&D at Boost Biomes, a biotech startup focused on bio-pesticides and bio-fertilizers. Garcia's passion for microbiology began studying soil remediation at Texas A&M University. Seeing microbes under the microscope for the first time felt like discovering "another world," sparking a lifelong fascination with what microbes are and can do. Driven by a desire to see her science make an immediate impact, Garcia was drawn to industry after completing her Ph.D. At Boost Biomes, a biotech startup company, Veronica helped transform diverse microbial isolates into bio-pesticides, bio-fertilizers and bio-stimulants for agriculture and food. She progressed from bench scientist to senior Director of R&D, overseeing discovery, genomics, bioinformatics and product development, and learned the realities of scale-up, cost, regulation and end-user needs. She also monitored air, water and surfaces for the shuttle and ISS and NASA, ensuring astronaut safety by tracking microbial loads and potential pathogens. ASM is organizing around 3 scientific units, ASM Applied and Environmental Microbiology (AEM), ASM Health and ASM Mechanism Discovery. These units will equip researchers to translate discovery into impact while providing a forum to collectively shape the future of the field. The AEM unit provides the space and unique expertise for microbial scientists and partners to directly contribute to a healthier, more sustainable world through applied and environmental innovation and brings together experts whose work connects microbial processes to outcomes in ecosystems, infrastructure, food systems and planetary health. Links For This Episode Learn More About ASM's Scientific Units. Join the Conversation on ASM Connect, our online community platform. Browse Volunteer Opportunities. Become an ASM Member. Take the MTM listener survey!

Marlene Belfort, Ph.D., a distinguished professor at the University at Albany and author of Mommy, Can Boys Also Be Doctors?, discusses her journey in science, balancing personal and professional life, the importance of fundamental research and the discovery of introns in bacteriophage. Links for This Episode Mommy, Can Boys Also Be Doctors?: A Message to Young Scientists and Other Humans.

Episode Summary Sue Ishaq, Ph.D., Associate Professor of Microbiomes at the University of Maine, discusses how gut microbes transform seemingly inert plant compounds—like glucosinolates found in broccoli—into powerful anti-inflammatory agents such as sulforaphane. Her research dives into the fascinating interplay between diet, cooking methods and the diversity of the gut microbiota, revealing how these factors influence the body's ability to produce health-promoting molecules. Links for This Episode mSystems paper: Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. mSystems paper: Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice. Current Developments in Nutrition paper: Current knowledge on the preparation and benefits of cruciferous vegetables as relates to in vitro, in vivo, and clinical models of Inflammatory Bowel Disease.

Karl Matthews, Ph.D., Professor of Microbial Food Safety at Rutgers University, discusses ways to eliminate pathogens like Salmonella, E. coli O157:H7 and Listeria from fresh fruits and vegetables. He highlights the importance of preventative measures from farm to table, including the use of water antimicrobials, like chlorine, and photosensitizers, like curcumin. Watch this episode: https://youtu.be/6Wkef9RyUVE Ashley's Biggest Takeaways We consume billions of microorganisms in the food that we eat each day. Fresh fruits and vegetables that are not thermally processed are likely to carry a higher microbial load than cooked foods. Many of those microbes are not concerning to human health. However, when pathogens of human health concern are present, the food can become unsafe to eat. Scientists use many methods from pre-harvest through post-harvest to keep food free of human pathogens. Water antimicrobials, such as chlorine, and photodynamic inactivation using photosensitizers, such as curcumin, are 2 preventative measures that Matthews and colleagues are investigating. Curcumin is a natural chemical compound found in the turmeric plant. It is responsible for giving tumeric its yellow color. Curcumin is also a photosensitizer, meaning that it can absorb light energy and transfer it to another molecule to initiate chemical reactions that produce cytotoxic singlet oxygen. Featured Quotes When I look at [what makes fruits and vegetables safe to eat] as far as from a microbiological perspective, it's are they free of pathogens of human health concern? And so, we might think about organisms, such as Salmonella or the Shiga toxin producing E coli or Listeria. There are a number of processes and initiatives that are put into place, from the pre-harvest through post-harvest levels to try to ensure that the product is not contaminated with microorganisms of human health concern. Each day, we're consuming literally billions of microorganisms in the foods that we eat, and particularly the raw fruits and vegetables that we're eating that are not being thermally processed in any fashion by which you might reduce the microbial load. Oftentimes we think about the bacteria that might well be there. But we do know that there's viruses that could be present. There's certain type of protozoa that might be present. Many of us know of norovirus and the concerns associated with that particular pathogen. So, there's a multitude of microorganisms that might well be associated with fresh fruits and vegetables, but there's really a very limited number or types that are actually of concern from a human health standpoint. In my program, we're working on E. coli O157:H7, in particular. It's a certain serotype of E. coli, a diarrheagenic E. coli, what's also known as a Shiga toxin-producing E. coli. We work with Salmonella, and we work with Listeria monocytogenes, but there's other microorganisms, such as Campylobacter, Yersinia, Staphylococcus aureus. All of those types of pathogens can also be associated with foods—and different types of foods, at that—and be of concern to the general public—the consumer. If we look at a lot of the processing of foods that are taking place, not only here in the United States, but globally, many times, what will happen is they're utilizing some type of a water antimicrobial, and I stress that because, oftentimes, these antimicrobials are added to the water to control the microbial load in the water. So, ultimately, you're not basically putting on water and putting on a whole load of microorganisms along with it. And also, you can prevent cross contamination through that. Here in the U.S. and elsewhere, we'll often put additional chlorine into the water. So, let's say we're increasing the chlorine concentration to 20 parts per million, or 50 parts per million, or maybe in poultry processing, they're utilizing peracetic acid. These are 2 common antimicrobials that are being used. What we wanted to do is find out could we utilize some other types of methods that might well control microorganisms on the commodity itself? And that's where we started looking at photodynamic inactivation and coupling that with the use of a photosensitizer. And in this particular case, the photosensitizer we were using was curcumin. The reason for working with curcumin is that it's naturally used in foods as a food dye. It's also used as a flavoring agent, and so forth. So, it's there, and it's being used—not just in the U.S., but [also] globally. And we thought we would try to see if we utilize this compound, could we have an additive effect to it? If you apply certain wavelengths of light, you can inactivate microorganisms, but if you apply that wavelength to something like a photosensitizer type molecule (curcumin), you could generate singlet oxygen molecules. And those singlet oxygen molecules would act like little explosions on the cell membrane and basically blow it apart and, therefore, inactivate the organism. We looked

Michael Lynch, Ph.D., Director of the Center for Mechanisms of Evolution at Arizona State University and Vaughn Cooper, Ph.D., professor of Microbiology and Molecular Genetics at the University of Pittsburgh, School of Medicine, examine the origins and trajectory of early microbial life (EML) and discuss the collaborative report between the American Academy of Microbiology and the Gordon and Betty Moore Foundation, which explores the journey of life on Earth, from non-living chemical compounds to early unicellular life, to the vast diversity of organisms we see today. This episode is brought to you by the American Academy of Microbiology, a think tank at American Society for Microbiology and the Gordon and Betty Moore Foundation, which has been dedicated to advancing scientific discovery for the past 25 years. Links for This Episode: Project Report Early Microbial Life: Our Past, Present and Future. Article: The Great Oxidation Event: How Cyanobacteria Changed Life. MTM Podcast: From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier. Take the MTM listener survey!

Sally Bornbusch, Ph.D., is an NSF postdoctoral fellow in biology conducting microbial ecology research in animal care and conservation at the Smithsonian National Zoo & Conservation Biology Institute. She discusses how FMTs are being used to mitigate health concerns in wild animals in captivity, shares key findings about the milk microbiome from the Smithsonian milk repository, the largest collection of exotic animal milks in the world, and explains the science behind eating poo (Coprophagia). Links for This Episode Why Do Animals Eat Poop? (And Why It Might Be a Good Thing). Faeces as food: a framework for adaptive nutritional coprophagy in vertebrates. Even Monkeys Should Eat Their Vegetables. Take the MTM listener survey!

Dev Mittar, Ph.D., Scientific Director of the ASM Health Scientific Unit discusses the use of metagenomic next generation sequencing to develop agnostic diagnostic technology, giving scientists and clinicians alike, a tool to diagnose any infectious disease with one single test. He also discusses how the ASM Health Unit is empowering scientists and leveraging microbial science innovations to address critical global health challenges and improve lives worldwide. Ashley's Biggest Takeaways The Division of Research, Innovation and Ventures is a small entrepreneurial arm of BARDA that takes on early-stage projects with high potential of turning into medical countermeasures. Prior to his role as Scientific Director for ASM Health, Mittar worked as a health scientist and program officer at DRIVe, where he focused on advancing high-impact science. He is particularly passionate about his work to develop agnostic diagnostics—a single test that uses metagenomic next generation sequencing to identify any pathogen from 1 clinical sample. Mittar discusses applications for this technology in surveillance (pandemic preparedness), variant detection, AMR and clinical settings (diagnosing complicated infections where etiology is not clearly defined). He also shares how a recent bout with illness emphasized the value and potential of this technology to save money, time, pain and suffering of the patient. Agnostic diagnostics can also help prevent the overuse/misuse of antibiotics, which are key factors in the spread of antimicrobial resistance. Furthermore, when this technology is coupled with the use of metatranscriptomics, it can provide information about the patient's immune profile that can be helpful in developing personalized treatment strategies, as opposed to a one-size-fits-all approach. ASM is organizing around 3 scientific units, ASM Health, ASM Mechanism Discovery and ASM Applied and Environmental Microbiology. These units will empower researchers and scientists to use science make a difference in the world and provide a forum for them to come together to shape the future of the field. Links for This Episode Learn More About ASM's Scientific Units. Join the Conversation on ASM Connect, our online community platform. Browse Volunteer Opportunities. Become an ASM Member. Register for ASM Microbe 2025.

Episode Summary Afreenish Amir, Ph.D., Antimicrobial Resistance (AMR) Project Director at the National Institute of Health in Pakistan, highlights significant increases in extensively drug-resistant typhoid and cholera cases in Pakistan and discusses local factors driving AMR in Asia. She describes the development and implementation of a National Action Plan to combat AMR in a developing country, emphasizing the importance of rational antimicrobial use, surveillance and infection control practice. Ashley's Biggest Takeaways AMR is a global and One Health issue. Pakistan has a huge disease burden of AMR. Contributing factors include, but are not limited to, overcrowding, lack of infection control practices, poor waste management practices and over-the-counter prescription practices. Promoting the rational use of antimicrobials is imperative at all levels—from tertiary care to primary care practitioners. Typhoid and cholera are high-burden infections in Pakistan, with typhoid being a year-round issue and cholera being seasonal. A holistic approach, involving various sectors and disciplines, is necessary in order to address the global AMR threat. Amir highlights the need for better communication and collaboration to bridge gaps and build trust between different organizations. Featured Quotes: I've been working at the National Institutes of Health for the last 7 years now. So, I've been engaged in the development and the implementation of the national action plan on AMR, and that gave me the opportunity to explore the work in the field of antimicrobial resistance. Reality of AMR in Pakistan [Pakistan] is an LMIC, and we have a huge disease burden of antimicrobial resistance in the country right now. A few years back, there was a situational analysis conducted, and that has shown that there is presence of a large number of resistant pathogens within the country. And National Institutes of Health, they have started a very standardized surveillance program based upon the global antimicrobial use and surveillance system back in 2017. And [those datasets have] generated good evidence about the basic statistics of AMR within the country. So, for example, if I talk about the extensively drug-resistant typhoid, typhoid is very much prevalent in the country. Our data shows that in 2017 there were 18% MDR typhoid cases through the surveillance data. And in 2021 it was like 60%. So that has shown that how the resistance has increased a lot. A number of challenges are associated with this kind of a thing, overcrowded hospitals, poor infection prevention and control (IPC) measures. So, there is AMR within the country—there's a huge burden—and we are trying to look for the better solutions. Local Factors Driving AMR Bacteria, they do not know the borders. We have a close connection with the other Asian countries, and we have a long border connected with the 2 big countries, which are Afghanistan and India and Bangladesh and China. So, we see that it's not limited to 1 area. It's not regional. It's also a history of travel. When the people travel from one area to the other, they carry the pathogen as a colonizer or as a carrier, and they can infect [other] people. So, it's really connected, and it's really alarming as well. You never know how the disease is transmitted, and we have the biggest example of COVID—how things have spread from 1 country to the other, and how it has resulted in a massive pandemic. AMR is similar. We have seen that it's not limited to 1 region. We are part of this global community, and we are contributing somehow to the problem. First, I'll talk about the health care infrastructure. We do have the capacities in the hospitals, but still, there's a huge population. Pakistan is a thickly populated country. It's a population of around 241 million. And with the increasing population, we see that the infrastructure has not developed this much. So now the existing hospitals are overcrowded, and this has led to poor infection control practices within the hospitals. The staff is not there. In fact, ID consultants are not available in all the hospitals. Infection control nurses are not available in all the hospitals. So, this is one of the main areas that we see, that there is a big challenge. The other thing that can contribute is the poor waste management practices. Some of the hospitals—private and public sectors—they are following the waste management guidelines—even the laboratories. But many of the hospitals are not following the guidelines. And you know that AMR is under one health. So, whatever waste comes from the hospital eventually goes to the environment, and then from there to the animal sector and to the human sector. [Another big] problem that we are seeing is the over-the-counter prescription of antimicrobials. There is no regulation available in the country right now to control the over-the-counter prescription of antibiotics. They are easily available. People are taking the antibiotics withou

Manuel Martinez Garcia, Ph.D., a professor of microbiology in the Physiology, Genetics and Microbiology Department at the University of Alicante in Spain, paints a picture of what microbial life looked like thousands of years ago by analyzing microbial genomic signatures within ice cores collected from the Antarctic ice shelves in the 1990s. Links for the Episode New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves – mSphere paper. Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles – Nature communications article. Manuel Martinez Garcia's Lab website. How stable is the West Antarctic Ice Shelf? – Press Release from Alfred Wegener Institute. Take the MTM listener survey! Watch this episode: https://youtu.be/CHCMO74_gIY Ashley's Biggest Takeaways There is a unique habitat beneath Antarctic ice shelves, where microbes live without light and rely on unusual energy sources. Ice cores from these Antarctic ice shelves can preserve fossilized genomic records of microbial life from long ago. Comparing past and present samples can help us understand how microbial life is responding to environmental stressors, like temperature changes and acidification, over time. It can also provide key insights to changes in biodiversity. Featured Quotes: Motivation for the Research Ice shelves are like massive floating ice that are in Antarctica, mainly. They can be as big as, for example, France, the country. So, they are super big—they are enormous. And they can be as thick as, let's say, 1000 meters. So, this is a massive [piece of] ice that we have in our planet. And beneath that massive ice, we can have a very peculiar and a special habitat in which microbes live without light. They have to manage, to thrive and reproduce, without using a standard energy like we have on the surface of the sea or in the forest, where we have light that is driving and providing the energy for the ecosystem. But in this case, these ecosystems are totally different. [The ice shelves] are deep and interconnected. Basically, there are different oceanic currents, for example, there is one Circumpolar Current that surrounds Antarctica, and there are also other currents that basically go from the bottom to the surface, moving, you know, all the water masses. The interesting part of this story is that every single second in our lives, this sea that is beneath the platform, the ice shelf, is frozen over and over, and then we have different layers of antiquity that preserve the microbes that are living in the ocean. So, for example, let's say, 1000 years ago, the sea water was frozen, and then we can find a layer beneath the Antarctica ice shelf, where these microbes are preserved and frozen. Basically, it's like a record—a library of microbes, fossil records of microbes—from the past ocean, from 1000 years ago until present, more or less. And then we can go to these records, to these layers of frozen sea water, and pick these samples to somehow recover the genetic material of the microbes that were preserved and frozen 1000 years ago or 500 years ago, in the way that we can somehow reconstruct or build the genetic story of the microbes from the past, for example, pre-industrial revolution to present. We need to think that microbes sustain the rest of the food web. So, they sustain of the rest of life in the ocean. They provide carbon for the rest of organisms, the fishes, whales [and other] big animals that we have in our oceans. And if the microbes are responding in a way that is not satisfactory, or in the way that we think can maintain the food web, this is kind of scary. And this is what we are trying to do: we are trying to go back to the past and see how the microbes are changing [genetically]. Sample Collection We didn't collect the samples. [They were collected] back in the 90s, so, 40 years ago, by a German group led by the Alfred Wegener Institute, which is probably one of the most famous polar institutes in the world. They, basically, led an expedition, I think it was in 92, and they decided to go to this ice shelf in Antarctica, in the Filchner–Ronne Ice Shelf to collect these ice cores. And then the surprise was when they were progressing in the drilling, they realized that on the top part of the ice core was fresh water, meteoric snow that was compacted forming the ice. But they realized that below that part, there was a sea water that was frozen. And then they thought that these samples were very interesting, because they somehow store material from the past, and they shipped these samples to Alfred Werner Institute in Bremerhaven in Germany. And half of the samples were stored for 40 years until I decided to contact the Institute and to propose this research. And I basically contacted the director of the Institute, and also the group of Frank Wilhelm, to propose the idea. And basically, I said, 'Hey, I think what you have in your research i

Episode Summary Mother-Son duo, Brenda Wilson, Ph.D., professor of microbiology and the Associate Director of Undergraduate Education in the School of Molecular and Cellular Biology at the University of Illinois at Urbana Champaign and Brian Ho, Ph.D., researcher and lecturer at the Institute of structural and molecular biology, a joint institute between the Department of structural and molecular biology at the University College of London and the Department of Biological Sciences at Birkbeck University of London discuss the inspiration and motivation for their recent book, Revenge of the Microbes: How Bacterial Resistance is Undermining the Antibiotic Miracle, 2nd Edition, emphasizing the global nature of AMR and providing a unique perspective on what is needed to solve it. Ashley's Biggest Takeaways: Dynamics surrounding the AMR crisis are complex and require an understanding of many different perspectives, including those of the farmers, health care professionals, pharmaceutical companies and individuals, in order to foster true and lasting global collaboration on the issue. Point-of-care diagnostics are critical to improving treatment decisions and reducing hospital costs. Better communication and education are needed in order to rebuild trust in scientists and institutions. Continuous research is necessary, as AMR will continue to evolve. Citizens are a key piece of the puzzle when it comes to pushing for change and supporting solutions to AMR. Featured Quotes: Wilson: "I'll start with actually my Ph.D., which is talking about bacterial antibiotic biosynthesis. And so, I did some work in that arena, but since then, I've actually been working on bacterial protein toxins. These are very potent eukaryotic modulators that when bacteria get into the host, they release these proteins that are very large, that are able to interact with very specific cells. They actually get inside the cells—into the cytosol—and then they affect various signaling pathways in the host that can go anywhere from killing the cell to modulating some of the processes that the cell undertakes, even differentiating them and causing cancer. So, one of my main focuses in my lab has always been to understand the structure and function of these toxins, to understand how they affect the eukaryotic cell system. And then now that we know a lot about them, we're actually moving more into the direction of trying to basically use them as biologics. We have some platforms that we call bacterial toxin inspired drug delivery, where we're using the mechanisms of how they work and their exquisite specificities to be able to actually use them for therapeutic applications." Ho: "I got my start doing molecular genetics, actually, with John Mekalanos at Harvard, and I was kind of at the ground floor of the seminal work looking at the Type VI secretion system. And so, I got a front row seat to the kind of discovery and a lot of the initial understanding of the system. And I've kind of taken that work and expanded beyond it to look at kind of the ways different bacteria interact with each other within microbial communities. So my current work is looking at both DNA conjugation as well as the type six antagonism, and how the bacterial interactions kind of work together to build a larger population dynamics and interface with like the hosts that kind of house a your microbial communities." Antimicrobial Resistance Wilson: "In 2005 [when the first edition of Revenge of the Microbes was written], there was very little activity or understanding about antibiotic resistance and how important it was. Outside of the field, doctors were encountering it. But oftentimes what was happening is they just said, 'Oh, well, we'll just find another drug, you know.' And pharmaceutical companies, they were recognizing that there was a problem, and they would go off trying to hunt for new ones. And then right around the late 90s, there was a big impetus, because they thought, 'Oh, we, we have a miracle here, because we now do complete genomes. We can get out the comparative genomics and all the high throughput things, all the animations,' and that this would lead to many more new discoveries. And I think the pharmaceutical companies were very disappointed, and they started backing out of what they deemed a huge commitment. Two decades later, people already were starting to get aware, at least in the field, and even the industry and the physicians. People were getting aware, but I think that they were stumbling, because of their silos, in trying to get interactions with each other. And I think part of it was that they felt that, 'Oh, we can try to solve it ourselves.' And in reality, this is a problem that that is concerning everyone, and everyone is contributing to it. Everyone has to find a solution to help, and we need to have more synergy. There have to be more interactions, and we have to do this at a much more global scale. And so that was sort of what, what we thought wh

Joseph James, biologist at the U.S. Environmental Protection Agency, discusses his career trajectory and the creation of Binning Singletons, a unique mentorship program built on peer-to-peer networking at scientific meetings and conferences and was first implemented in 2019 at ASM Microbe. Links for the Episode Binning Singletons and Peer-to-Peer Networking Learn more about Binning Singletons. Contact Joe James: [email protected] Follow Binning Singletons on Bluesky. Binning Singletons: Mentoring through Networking at ASM Microbe 2019—mSphere article. Binning Singletons: Tackling Conference Networking When You Don't Know Anyone—Guest post on Addgene Blog. Mastering a Mentoring Relationship as the Mentee—asm.org article that James says has really helped him explain Binning Singletons as a coaching form of mentorship. Mapping a Mentoring Roadmap and Developing a Supportive Network for Strategic Career Advancement—article on developing networks of mentors, another area Binning Singletons tries to address. #FEMSmicroBlog: Networking at Online Conferences (for Early Career Scientists). Take the MTM listener survey! James' Research Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil. In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary. Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach. Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes. Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.

Saeed Khan, Ph.D., Head of the Department of Molecular Pathology at Dow diagnostic research and reference laboratory and President of the Pakistan Biological Safety Association discusses the importance and challenges of biosafety/biosecurity practices on both a local and global scale. He highlights key steps for biorisk assessment and management and stresses the importance of training, timing and technology. Ashley's Biggest Takeaways Adequate biosafety and biosecurity protocols depend on a thorough understanding of modern challenges, and scientists must be willing and able to respond to new technological threats appropriately. In the microbiology lab, the threat goes beyond the physical pathogen. Implications of genomics and cyber security must be built into biorisk management techniques, including data storage and waste management practices. Risk assessments involve evaluation of both inherent and residual risk. Inherent risk is linked to the pathogen. Residual risk varies according to the lab, equipment, employee, environment, etc. As a result, biosafety and biosecurity risks are constantly changing, and assessments must be repeated strategically and often. Khan recommended repeating a risk assessment whenever a key variable in the equation changes, i.e., new equipment, new employee, new pathogen. He also recommended (at minimum) conducting routine risk assessments every 6 months, or twice a year. Featured Quotes: "We need to have basic biosafety and biosecurity to stay away from these bugs and the modern challenges, like cyber biosecurity and genomics. These are the new areas, which are potential threats for the future, and where we need to train our researchers and students." "Starting from simple hand washing or hand hygiene, the basic things we use are gloves, goggles and PPE to protect the workers, the staff and the patient from getting infected from the environment, laboratory or hospitals. These are the basic things, and it's very crucial, because if one is not using gloves in the lab or not wearing the lab coat, he or she may get infected from the sample, and the patient can get infected from the physician and doctors or nurse if they are not following the basic biosafety rules. These [things] are routinely important. Every day we should practice this." "But there are [also] new challenges. Particularly in the microbiology lab, we [used to] think that once we killed the bacteria, then it's fine. But nowadays, it's not the way we should think about it. Though you kill the bacteria practically, it still has a sequence, [which] we call the genome, and if you have that information with you, you theoretically have the potential to recreate that pathogen… that can be used or maybe misused as well." "[Working with] scripts of pathogens, like smallpox or the polioviruses, we call this synthetic biology. Different scientists are doing it for the right purposes, like for production of vaccines, to find new therapeutics, to understand the pathology of the diseases. But on [the other hand]—we call it dual use research of concern (DURC)—the same can be misused as well. That's why it's very important to be aware of the bugs that we are working with, and the potential of that pathogen or microbe, to the extent that can be useful or otherwise." "So, we should be aware of the new concern of the technology, synthetic biology and DURC. These are new concepts—cyber, biosecurity and information security [are all] very much important these days. You cannot be relaxed being in the microbiology lab. Once we have identified a pathogen, declared a result to the patient and the physician, and it's been treated, we [still] need to be worried about waste management—that we discard that waste properly and we have proper inventory control of our culture. It should be safe in the locker or on in the freezers and properly locked, so we should not be losing any single tube of the culture, otherwise it may be misused." Risk Assessment "The best word that you have used is risk assessment. So, it should gage the severity of the issue. We should not over exaggerate the risk, and we should not undermine the risk. Once the risk assessment been made, we can proceed." "Right from the beginning of touching a patient or a sample of the patient until the end of discarding the sample, that is called biorisk management. It's a complete science that we need to be aware of—not in bits and pieces. Rather a comprehensive approach should be adopted, and each and every person in the organization should be involved. Otherwise, we may think [we are] doing something good, but someone else may spoil the whole thing, and it will be counterproductive at the end." "We should involve each and every person working with us and the lab, and we should empower them. They should feel ownership that they are working with us, and they are [as] responsible as we are. So, this the whole process needs to be properly engaged. People must be engaged, and they should be

Nicole Dubilier, Ph.D., Director and head of the Symbiosis Department at the Max Planck Institute for Marine Microbiology, has led numerous reserach cruises and expeditions around the world studying the symbiotic relationships of bacteria and marine invertebrates. She discusses how the use of various methods, including deep-sea in situ tools, molecular, 'omic' and imaging analyses, have illuminated remarkable geographic, species and habitat diversity amongst symbionts and emphasizes the importance of discovery-driven research over hypothesis-driven methods. Watch this episode: https://www.youtube.com/watch?v=OC9vqE1visc Ashley's Biggest Takeaways: In 1878, German surgeon, botanist and microbiologist, Heinrich Anton de Bary, first described symbiosis as the living together of two or more different organisms in close physical intimacy for a longer period of time. These relationships can be beneficial, detrimental or commensal, depending on the organisms involved. Microbial symbiosis research holds great potential to contribute to sustainable energy production and environmental health. Links for This Episode: Learn more about one of Dubilier's research vessels and see videos from the expidition. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Chemosynthetic symbioses: Primer. Take the MTM listener survey!

From Bovine Spongiform Encephalopathy (BSE) to Creutzfeldt-Jakob disease (CJD), Neil Mabbott, Ph.D., has worked for nearly 2 decades on understanding the mechanisms by which prion proteins become infectious and cause neurological disease in humans and animals. He discusses the remarkable properties of prions and addresses complexities surrounding symptoms, transmission and diagnosis of prion disease.

Episode Summary Timothy Donohue, Ph.D.—ASM Past President, University of Wisconsin Foundation Fetzer Professor of Bacteriologyand Director of the Great Lakes Bioenergy Research Center (GLBRC) calls genomics a game-changer when it comes the potential of microbes to create renewable resources and products that can sustain the environment, economy and supply chain around the world. He also shares some exciting new advances in the field and discusses ways his research team is using microorganisms as nanofactories to degrade lignocellulose and make a smorgasbord of products with high economic value. Take the MTM listener survey! Ashley's Biggest Takeaways: The bioeconomy can be broadly defined as the use of renewable resources, including microorganisms, to produce valuable goods, products and services. Microbes have the potential to create products that cannot be made by existing synthetic chemistry routes. Using raw, renewable resources to create a circular bioeconomy is beneficial to the environmental footprint, economic footprint and supply chain security around the globe. Links for This Episode: The theme of our Spring 2024 Issue of Microcosm, our flagship member magazine is Microbes and the Bioeconomy: Greasing the Gears of Sustainability, launches this week and features an article based on this MTM conversation. If you are an ASM Member, check back on Wed., June 30 for the newly published content! Not a member? Consider renewing or signing up today, and begin exploring endless potential to boulster your career and network with professionals, like Donohue, in your field. Get Bioeconomy Policy Updates. Heading to ASM Microbe 2024? Check out this curated itinerary of sessions on the bioeconomy, including those discussing the use of algae for bioproduction and synthetic biology for natural product discovery. Learn more about the Great Lakes Bioenergy Research Center. MTM listener survey!

Rodney Rohde, Ph.D., Regents' Professor and Chair of the Medical Laboratory Science Program at Texas State University discusses the many variants, mammalian hosts and diverse neurological symptoms of rabies virus. Take the MTM listener survey! Ashley's Biggest Takeaways: Prior to his academic career, Rohde spent a decade as a public health microbiologist and molecular epidemiologist with the Texas Department of State Health Services Bureau of Laboratories and Zoonosis Control Division, and over 30 years researching rabies virus. While at the Department of Health Lab, Rohde worked on virus isolation using what he described as "old school" cell culture techniques, including immunoassays and hemagglutinin inhibition assays. He also identified different variants of rabies virus, using molecular biology techniques. Rohde spent time in the field shepherding oral vaccination programs that, according to passive surveillance methods have completely eliminated canine rabies in Texas. In the last 30-40 years, most rabies deaths in the U.S. have been caused by bats. Approximately 98% of the time rabies is transmitted through the saliva via a bite from a rabid animal. Post-exposure vaccination must take place before symptoms develop in order to be protective. Links for This Episode: Molecular epidemiology of rabies epizootics in Texas. Bat Rabies, Texas, 1996–2000. The Conversation: Rabies is an ancient, unpredictable and potentially fatal disease. Rohde and Charles Rupprecht, 2 rabies researchers, explain how to protect yourself. The One Health of Rabies: It's Not Just for Animals. MTM listener survey!

ASM's Young Ambassador, Aureliana Chambal, discusses the high incidence of tuberculosis in Mozambique and how improved surveillance can help block disease transmission in low resource settings. Ashley's Biggest Takeaways: Mozambique is severely impacted by the TB epidemic, with one of the highest incidences in Africa (368 cases/ 100,000 people in the population). Human-adapted members of the Mycobacterium tuberculosis complex (MTBC) belong to 7 different phylogenetic lineages. These 7 lineages may vary in geographic distribution, and have varying impacts on infection and disease outcome. For decades, 2 reference strains have been used for TB lab research, H37Rv, which Chambal mentions, and Erdman. Both of these belong to TB Lineage 4. According to Chambal, the reference strains that we use for whole genome sequencing (worldwide) may be missing genes that are related the virulence (and/or resistance) of strains that are circulating in a given population and detected in clinical settings. Chambal is endeavoring to employ a new strain to control these analyses and better understand transmission dynamics in the community setting. Featured Quotes: The Schlumberger Foundation Faculty for the Future Fellowship is one of my proudest accomplishments for the 2023. I applied for this fellowship last year to pursue my Ph.D. It is a program that supports women coming from emerging and developing economies to pursue advanced research qualifications in science, technology, engineering and mathematics. I applied because I was looking to get more skills in microbiology, specifically tuberculosis, to pursue my Ph.D. at Nottingham Trent University. Pathway to Microbiology Research My trajectory is different because I have a bachelor's in veterinary medicine. And during my undergrad, I always had more interest in the lab practice modules or disciplines. For the end of the [bachelor's] project, I was looking to understand the anthelmintic effectiveness against the gastrointestinal parasites in goats. After I finished this project, I was looking to continue a related project, but unfortunately, I couldn't get work related to that.. In 2016, I applied for the National Institutes of Health of Mozambique, which is one of the biggest research institutions in my home country. That's when I was selected to work at the north region of Mozambique, specifically at the Nampula Tuberculosis Reference Laboratory. And then I moved to the public health laboratory as well, where I had the opportunity to work in the microbiology section. So, to be honest, my passion for microbiology started when I had the first contact with the TB lab, and then I couldn't separate myself from this area, tuberculosis. In 2016, I had the opportunity to receive a mentorship. Our lab, the TB lab of Nampula, received mentorship from the American Society for Microbiology. And we worked with Dr. Shirematee Baboolal; she was the mentor of our lab. The main idea of the program was to get the lab accredited and to build technical capacity in the lab. And to be honest, at the time, I didn't have much experience in lab techniques to detect or diagnosis tuberculosis. And I said to Dr. Shirematee, "I don't have much experience in this area, so, I don't know if I will be able to help you to accomplish these goals." And she said, "If you want to learn, I can teach you, and you can be one of the best in this area." And then we started training with her. It was very interesting. The passion she passed to us about microbiology—and tuberculosis, in particular—was one of the triggers for my passion in this area. So, to be honest, Dr. Shirematee Baboolal was one of the persons that triggered my interest from tuberculosis. So, I have to say thank you to her! Tuberculosis Genomic Diversity and Transmission Dynamics Mozambique is one of the higher burden countries of tuberculosis. So, our population is about 33 million people. And the case rate is high, it is approximately 360 per 100,000 people in the population, which is equivalent to over 110,000, which is equivalent 211,000 cases in the population. So, while I was working for the TB lab, I always had the desire to understand more about the transmission of the disease in the community. And I felt like I didn't have enough skills to do that; I didn't the tools to do that. And I said, "Okay, let me try to look to improve the skills." That's why for my master's degree I tried to understand the genomic diversity of M. tuberculosis and see how we can see the gene content diversity within the lineage for which is the most spread lineage worldwide, and is predominant in Mozambique. Afterwards, I tried to expand to the other lineages. When I finished my master's degree, I felt that it was still missing something. I had the information about [TB] diversity, but I didn't get the point about transmission itself. That's why, when I went back and applied for my Ph.D., I structured my current project to specifically look at transmission and trans

The scientific process has the power to deliver a better world and may be the most monumental human achievement. But when it is unethically performed or miscommunicated, it can cause confusion and division. Drs. Fang and Casadevall discuss what is good science, what is bad science and how to make it better. Get the book! Thinking about Science: Good Science, Bad Science, and How to Make It Better

Dr. James Morton discusses how the gut microbiome modulates brain development and function with specific emphasis on how the gut-brain axis points to functional architecture of autism. Watch James' talk from ASM Microbe 2023: Using AI to Glean Insights From Microbiome Data https://youtu.be/hUQls359Spo

Dr. Michael ginger, Dean of the School of Applied Sciences in the Department of Biological and geographical Science at the University of Huddersfield, in West Yorkshire, England discusses the atypical metabolism and evolutionary cell biology of parasitic and free-living protists, including Leishmania, Naegleria and even euglinids.

Dr. Maria Eugenia Inda-Webb, Pew Postdoctoral Fellow working in the Synthetic Biology Center at MIT builds biosensors to diagnose and treat inflammatory disorders in the gut, like inflammatory bowel disease and celiac disease. She discusses how "wearables," like diagnostic diapers and nursing pads could help monitor microbiome development to treat the diseases of tomorrow. Subscribe (free) on Apple Podcasts, Spotify, Google Podcasts, Android, RSS or by email. Ashley's Biggest Takeaways Biosensors devices that engineer living organisms or biomolocules to detect and report the presence of certain biomarkers. The device consists of a bioreceptor (bacteria) and a reporter (fluorescent protein or light). Inda-Webb's lab recently published a paper in Nature about using biosensors (Sub-1.4 cm3 capsule) to detect inflammatory biomarkers in the gut. The work is focused on diagnosing and treating inflammatory bowel disease, but Inda-Webb acknowledged that that is a large research umbrella. The next step for this research is to monitor the use of the biosensor in humans to determine what chemical concentrations are biologically relevant and to show that it is safe for humans to ingest the device. It is believed that the gut microbiome in humans develops in the first 1000 days to 3 years of life. Early dysbiosis in the gut has been linked to disease in adulthood. However, we do not have a good way to monitor (and/or influence) microbiome development. Inda-Webb hopes to use biosensors in diapers (wearables) to monitor microbiome development and prevent common diseases in adulthood. In 2015, Inda-Webb became ASM's first Agar Art Contest winner for her piece, "Harvest System." Inda-Webb is the 2023 winner of the ASM Award for Early Career Environmental Research, which recognizes an early career investigator with distinguished research achievements that have improved our understanding of microbes in the environment, including aquatic, terrestrial and atmospheric settings. Learn More About ASM's Awards Program Featured Quotes: We engineer bacteria to sense particular molecules of interest—what we call biomarkers—if they are associated with a disease. And then, we engineer a way that the bacteria will produce some kind of molecule that we can measure—what we call reporter—so that could be a fluorescent protein or light, like the one that we have in this device. The issue is that inflammation in the gut is really very difficult to track. There are no real current technologies to do that. That is like a black box. And so, most of what we measure is what comes out from the gut, and has its limitations. It doesn't really represent the chemical environment that you have inside, especially in areas where you're inflamed. So, we really needed technologies to be able to open a window in these areas. The final device that I am actually bringing here is a little pill that the patient would swallow and get into the gut. And then they engineer bacteria that the biosensors, will detect, let's say, nitrous oxide, which is a very transient molecule. And the bacteria are engineered to respond to that in some way—to communicate with the electronics that will wirelessly transmit to your cell phone. And from there, to the gastroenterologist. We make the bacteria produce light. If they sense nitrous oxide, they produce light, the electronics read that, and the [information] finally gets into your phone. Part of the challenge was that we needed to make the electronics very very tiny to be able to fit inside the capsule. And also, the amount of bacteria that we use also is only one microliter. And so, imagine one microliter of bacteria producing a tiny amount of light. Finally, the electronics need to be able to read it. So that has been also part of the challenge. In this case, you have 4 different channels. One is a reference, and then the other 3 are the molecule of your choice. So, for example, what we show in the paper here is that we can even follow a metabolic pathway. So, you can see one more molecule turn into the other one, then into the other one. I'm really excited about that. Because normally we kind of guess as things are happening, you know, but here you can see in real time how the different molecules are changing over time. I think that's pretty exciting for microbiologist. The immediate application would be for a follow up. Let's say the patient is going to have a flare, and so you could predict it more much earlier. Or there's a particular treatment, and you want to see what is happening [inside the gut]. But for me, as a microbiologist, one of the things I'm most excited about will be more in the longer term. One of my favorite experiments that I do with the students is the Winogradsky column, and everyone gets super excited. So, we all have nice feelings for that. And it's basically a column where we asked the students to bring mud from a lake, for example, and then some sources of nutrients. And then, after 6months, you will

Dr. Gary Procop, CEO of the American Board of pathology and professor of pathology at the Cleveland Clinic, Lerner School of Medicine discusses the importance of early detection and diagnosis in order to prevent fungal invasion leading to poor outcomes, particularly in immunocompromised patients. He emphasizes the importance of thinking fungus early, shares his passion for mentoring and talks about key updates in the recently released 7th Edition of Larone's Medically Important Fungi. Ashley's Biggest Takeaways Many invasive fungal infections are angiotrophic, meaning they actually grow toward, and into, blood vessels. Once the fungus has penetrated the blood vessel, the blood essentially clots, causing tissue downstream from the blood clot to die (infarction). When tissues that have been excised are viewed under the microscope, hyphal elements can be seen streaming toward or invading through the wall of the blood vessels. Once the clot forms, those hyphal elements can be seen in the center of the blood vessel where only blood should be. Antifungals cannot be delivered to areas where the blood supply has stopped. Therefore, treatment requires a combined surgical and medical approach, and the process is very invasive. Early detection can prevent these bad outcomes by allowing antifungal treatment to be administered before angioinvasion occurs. Links for the Episode: Expand your clinical mycology knowledge with the recently released 7th edition of Larone's Medically Important Fungi: A Guide to Identification. Written by a new team of authors, Lars F. Westblade, Eileen M. Burd, Shawn R. Lockhart and Gary W. Procop, this updated edition continues the legacy of excellence established by founding author, Davise H. Larone. Since its first edition, this seminal text has been treasured by clinicians and medical laboratory scientists worldwide. The 7th edition carries forward the longstanding tradition of providing high-quality content to educate and support the identification of more than 150 of the most encountered fungi in clinical mycology laboratories. Get your copy today with $1 flat rate shipping within the U.S. or order the e-book! ASM members enjoy 20% off at checkout using the member promo code. Let us know what you thought about this episode by tweeting at us @ASMicrobiology or leaving a comment on facebook.com/asmfan.

From antifungal resistance to disaster microbiology and tales of visible mold growing across the skin of patients following a tornado in Joplin, Missouri, Dr. Shawn Lockhart, Senior Clinical Laboratory Advisor in the Mycotic Diseases Branch at the CDC talks all things fungi—complete with references to pop TV shows and the recently released 7th Edition of Larone's Medically Important Fungi. Links mentioned: Larone's Medically Important Fungi: A Guide to Identification, 7th Edition (Use code: MCR20 at checkout for 20% off) CDC's Mycotic Diseases Branch conducts an annual training course on the identification of pathogenic molds.

Dr. Kate Howell, Associate Professor of Food Chemistry at the University of Melbourne, Australia discusses how microbes impact the flavor and aroma of food and beverages and shares how microbial interactions can be used to enhance nutritional properties of food and beverage sources. Ashley's Biggest Takeaways Saccharomyces means sugar-loving fungus. Humans have similar olfactory structures and mechanisms as insects and are similarly attracted to fermenting or rotting fruits produced by Saccharomyces. Research has shown that insects (and humans) prefer yeasts that produce more esters and aromatic compounds. Palm wine is a product that is made from sap collected from palm trees (palm sap) across the tropical band of the world. Fruity flavors appear to be less important to persistence of Saccharomyces strains in an Indonesian palm wine fermentation. This may be because palm wine fermentation is very quick, generally 1-3 days often, with a maximum of 5 days for fermentation to be conducted. Wineries, on the other hand, ferment annually (one fermentation per year/vintage), when the grapes are right. Grape wine fermentations can take 7 days to 2 weeks to complete. So different selections likely take place between the 2 fermentation products. Featured Quotes: When we start drawing our lens on how microbes produce food for humans, we're coopting a process that happens quite naturally. Here I'll start off talking about Saccharomyces cerevisiae, the main fermenting yeast in food and beverage production, because it's one of the most studied organisms and was the first eukaryote to be sequenced. Saccharomyces cerevisiae, as the name implies, loves sugar, and it flourishes when there's a lot of sugar in the environment. Where is sugar found? In fruits, and that's done quite deliberately, because fruits develop sugars and flavors and aromas to attract a birds or insects or anything else that can carry their seeds elsewhere for dispersal. Now, Saccharomyces lies dormant in the environment in a spore before it encounters a sugar-loving environment. And then it replicates very quickly and tends to dominate fermentation. Humans have coopted that into our kitchens, into our meals, into our lives, and we use that process to produce food. As Saccharomyces starts to use this sugar, it balances up its metabolism. And as it does this, it produces aromas. These aromas have a lot of important characteristics. Humans love them, but insects also love them too. I've been interested in the yeasts that are found naturally in sourdough starters. Sourdough is a really interesting system. Because you've got yeast and bacteria interacting with one another. One of the things we are collaborating on with colleagues in France at Inrae, Dr. Delphine Sicard, is to understand some of the non-Saccharomyces yeasts that are naturally occurring in sourdough starters. So here we're looking at a collection of a yeast called Kazachstania humilis and trying to understand how it has adapted to the sourdough environment, how its sustained over time and how different global populations differ to one another. And this, of course, is of interest to the baking industry because not only do artisanal bakers have sort of an undiscovered wealth of biodiversity in their starters, baking companies also have an interest in using different sorts of flavors and bread for the commercial markets. The connection between a chemical profile and a person's sensory preference isn't something that's complete and direct. So, in every method that we use, there's always caveats, but we try to correlate it. Let's start off with the chemical characterization. We use headspace sampling, analytical chemistry, separation with gas chromatography and identification with mass spectrometry. And we use different 2-dimensional methods to be able to understand what the very small compounds are, and to be able to identify them. We can semi-quantify these to be able to make comparisons between different fermentations. We know from wine fermentations and understanding preferences of wine that, in some cases, a particular increase, or an abundance of a particular compound, can be extremely attractive. And that might depend on the style of wine. What we've discovered through this process is that different people prefer different flavors. Makes sense, doesn't it? We like different things. But some really interesting results from our lab, show that people from different cultural backgrounds have different preferences. And here we're using here in Melbourne, I'm very lucky to work with some very talented postdocs and Ph.D. students from China, who have very different preferences for wine than an Australian does. Of course, Australians are quite heterogeneous in their in their cultural diversity as well. But there's certain flavors that our Chinese colleagues tend to prefer. So we decided to investigate this a little bit more. So for this study, we recruited wine experts from Australia, actively worki

Dr. Steve Diggle, ASM Distinguished Lecturer and Microbiology Professor at the Georgia Institute of Technology in Atlanta, Georgia and Dr. Freya Harrison, Associate Microbiology Professor at the University of Warwick in Coventry, U.K., discuss the science behind medieval medical treatments and the benefits of interdisciplinary research. Ashley's Biggest Takeaways Diggle and Harrison met in Oxford, where Harrison was finishing up her Ph.D. and Diggle was doing background research for his work studying evolutionary questions about quorum sensing. When Diggle began searching for a postdoc, Harrison, who had been conducting an independent fellowship at Oxford and studying social evolution, applied. The AncientBiotics Consortium is a group of experts from the sciences, arts and humanities, who are digging through medieval medical books in hopes of finding ancient solutions to today's growing threat of antibiotic resistance. The group's first undertaking was recreation and investigation of the antimicrobial properties of an ancient eyesalve described in Bald's Leechbook, one of the earliest known medical textbooks, which contains recipes for medications, salves and treatments. The consortium found that the eyesalve was capable of killing MRSA, a discovery that generated a lot of media attention and sparked expanded research efforts. The group brought data scientists and mathematicians into the consortium (work driven by Dr. Erin Connelly from the University of Warwick). Together, the researchers began scouring early modern and medieval texts and turning them into databases. The goal? To mathematically data mine these recipes see which ingredients were very often or non-randomly combined in ancient medical remedies. The group recently published work showing synergistic antimicrobial effects of acetic acid and honey. They are also working to pull out the active compounds from Bald's eyesalve and make a synthetic cocktail that could be added to a wound dressings. A 1,000-Year-Old Antimicrobial Remedy with Antistaphylococcal Activity. Medieval medicine: the return to maggots and leeches to treat ailments. A case study of the Ancientbiotics collaboration. Phase 1 safety trial of a natural product cocktail with antibacterial activity in human volunteers. Sweet and sour synergy: exploring the antibacterial and antibiofilm activity of acetic acid and vinegar combined with medical-grade honeys. Let us know what you thought about this episode by tweeting at us @ASMicrobiology or leaving a comment on facebook.com/asmfan.

Dr. Jessica Lee, scientist for the Space Biosciences Research Branch at NASA's AIMS Research Center in Silicon Valley uses both wet-lab experimentation and computational modeling to understand what microbes really experience when they come to space with humans. She discusses space microbiology, food safety and microbial food production in space and the impacts of microgravity and extreme radiation when sending Saccharomyces cerevisiae to the moon. Ashley's Biggest Takeaways Lee applied for her job at NASA in 2020. Prior to her current position, she completed 2 postdocs and spent time researching how microbes respond to stress at a population level and understanding diversity in microbial populations. She has a background in microbial ecology, evolution and bioinformatics. Model organisms are favored for space research because they reduce risk, maximize the science return and organisms that are well understood are more easily funded. Unsurprisingly, most space research does not actually take place in space, because it is difficult to experiment in space. Which means space conditions must be replicated on Earth. This may be accomplished using creative experimental designs in the wet-lab, as well as using computational modeling. Links for the Episode: Out of This World: Microbes in Space. Register for ASM Microbe 2023. Add "The Math of Microbes: Computational and Mathematical Modeling of Microbial Systems," to your ASM Microbe agenda. Let us know what you thought about this episode by tweeting at us @ASMicrobiology or leaving a comment on facebook.com/asmfan.

Dr. Maria Gloria Dominguez-Bello, Henry Rutgers Professor of Microbiome and Health and director of the Rutgers-based New Jersey Institute for Food, Nutrition and Health, and Dr. Martin Blaser, Professor of Medicine and Pathology and Laboratory Medicine and director of the Center for Advanced Biotechnology and Medicine at Rutgers (NJ) discuss the importance of preserving microbial diversity in the human microbiome. The pair, whose research was recently featured in a documentary The Invisible Extinction, are on a race to prevent the loss of ancestral microbes and save the bacteria that contribute to human health and well-being. Links for the Episode: The Invisible Extinction (documentary) Missing Microbes (book) Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues (article) (YouTube) Missing Microbes with Dr. Martin Blaser

Dr. Robert Gaynes, distinguished physician and professor of infectious diseases at Emory University, joins Meet the Microbiologist for the 3rd , and final, episode in a unique 3-part segment, in which we share stories about the life and work of medial pioneers in infectious diseases. Here we discuss the career of Dr. Barry Marshall, the Australian physician who is best known for demonstrating in a rather unorthodox way that peptic ulcers are caused by the bacterium, Helicobacter pylori. Gaynes is author of Germ Theory: Medical Pioneers in Infectious Diseases, the 2nd edition of which will publish in Spring 2023. All 3 scientists highlighted in this special MTM segment are also featured in the upcoming edition of the book.

Dr. Robert Gaynes, distinguished physician and professor of infectious diseases at Emory University, joins Meet the Microbiologist for the 2nd episode in a unique 3-part series, in which we share the impact of scientists at the heart of various paradigm shifts throughout scientific history. Here we discuss the life and career of Tony Fauci, the scientist who has been recognized as America's Top Infectious Diseases Doctor and "voice of science" during the COVID-19 pandemic. Ashley's Biggest Takeaways Fauci was born in Brooklyn, New York. He was a 2nd generation American whose parents came from Italy. Fauci's father was a pharmacist in Brooklyn and was very influential in his life. During high school, Fauci worked behind the counter at the family pharmacy and even delivered prescriptions by bicycle. He attended a Jesuit high school in Manhattan, and attended the College of Holy Cross. After college, Fauci attended Cornell Medical School in Manhattan, which was his first choice of medical school. Fauci graduated first in his class in medical school in the mid 1960's, right in the midst of the Vietnam War. During that time, after completing their initial residency training, virtually all doctors were drafted into one of the military services or the U.S. Public Health Service. Fauci accepted into the NIH program within the U.S. Public Health Service, where he acquired training and a fellowship in Clinical Immunology and Infectious Diseases. Fauci became the Director of the National Institute of Allergy and Infectious Disease (NIAID) in 1984. Fauci served as advisor to 7 U.S. presidents, including Ronald Regan, George H.W. Bush, Bill Clinton, George W. Bush, Barack Obama, Donald Trump and Joe Biden. 15 years after the creation of PEPFAR, Fauci reported, in the New England Journal of Medicine, that PEPFAR funded programs had provided antiretroviral therapy to 13.3 M people, averted 2.2 M perinatal HIV infections and provided care for more than 6.4 M orphans and vulnerable children. The first edition of "Germ Theory: Medical Pioneers in Infectious Diseases" is available now. The 2nd edition will publish in the spring of 2023.

Dr. Robert Gaynes, distinguished physician and professor of infectious diseases at Emory University, joins Meet the Microbiologist for a unique episode, in which we share the story of Françoise Barré-Sinoussi, the French, female scientist who discovered HIV and found herself at the heart of one of the most bitter scientific disputes in recent history. Subscribe (free) on Apple Podcasts, Spotify, Google Podcasts, Android, RSS or by email. Ashley's Biggest Takeaways The U.S. Centers for Disease Control and Prevention (CDC)'s Morbidity and Mortality Weekly Report first reported on a cluster of unusual infections in June of 1981, which would become known as AIDS. Evidence suggested that the disease was sexually transmitted and could be transferred via contaminated blood supply and products, as well as contaminated needles, and could be passed from mother to child. All hemophiliacs of this generation acquired AIDS (15,000 in the U.S. alone). The fact that the microbe was small enough to evade filters used to screen the clotting factor given to hemophiliacs indicated that the etiologic agent was a virus. AIDS patients had low counts of T-lymphocytes called CD4 cells. By 1993, the most likely virus candidates included, a relative of hepatitis B virus, some kind of herpes virus or a retrovirus. Howard Temin discovered reverse transcriptase, working with Rous sarcoma in the 50s and 60s. His work upset the Central Dogma of Genetics, and at first people not only did not believe him, but also ridiculed him for this claim. Research conducted by David Baltimore validated Temin's work, and Temin, Baltimore and Renato Dulbecco shared the Nobel Prize for the discovery in 1975. Robert Gallo of the U.S. National Institute of Health (NIH), discovered the first example of a human retrovirus—human T-cell lymphotropic virus (HTLV-1). Françoise Barré-Sinoussi worked on murine retroviruses in a laboratory unit run by Luc Montagnier, where she became very good at isolating retroviruses from culture. In 1982, doctors gave lab Montagnier's lab a sample taken from a with generalized adenopathy, a syndrome that was a precursor to AIDS. Barré-Sinoussi began to detect evidence of reverse transcriptase in cell culture 2 days after the samples were brought to her lab. Barré-Sinoussi and Luc Montagnier were recognized for the discovery of HIV with the 2008 Nobel Prize in Physiology or Medicine. Links for the Episode: From the ancient worlds of Hippocrates and Avicenna to the early 20th century hospitals of Paul Ehrlich and Lillian Wald to the modern-day laboratories of François Barré-Sinoussi and Barry Marshall, Germ Theory brings to life the inspiring stories of medical pioneers whose work helped change the very fabric of our understanding of how we think about and treat infectious diseases. Germ Theory: Medical Pioneers in Infectious Diseases The second edition of Germ Theory, which will include chapters on Françoise Barré-Sinoussi, Barry Marshall and Tony Fauci, will publish in Spring 2023.

Episode Summary Dr. Devin Drown, associate professor of biology and faculty director of the Institute of Arctic Biology Genomics Core at the University of Alaska Fairbanks, discusses how soil disturbance gradients in the permafrost layer impact microbial communities. He also explains the larger impacts of his research on local plant, animal and human populations, and shares his experience surveilling SARS-CoV-2 variants in Alaska, where he and colleagues have observed a repeat pattern of founder events in the state. Ashley's Biggest Takeaways Permafrost is loosely defined as soil that has been frozen for 2 or more years in a row. Some permafrost can be quite young, but a lot of it is much older—1000s of years old. This frozen soil possesses large storage capacity for walking carbon and other kinds of nutrients that can be metabolized by microbes as well as other organisms living above the frozen ground. About 85% of the landmass in Alaska is underlined by permafrost. Some is continuous permafrost, while other areas of landmass are discontinuous permafrost—locations where both unfrozen soil and frozen soil are present. As this frozen resource is thawing as a result of climate change, it is releasing carbon and changing soil hydrology and nutrient composition, in the active layer in the soil surrounding it. Changes in the nutrients and availability of those nutrients are also likely changing the structure of the microbial communities. Drown and team are using a combination of traditional (amplicon sequencing) and 3rd generation (nanopore) next sequencing (NGS) techniques to characterize the microbes and genes that are in thawing permafrost soil. Featured Quotes: "Globally, we've seen temperatures increase here in the Arctic. Changes in global temperatures are rising even faster, 2-3 times, and I've heard recent estimates that are even higher than that." "These large changes in temperatures are causing direct impacts on the thaw of the permafrost. But they're also generating changes in other patterns, like increases in wildfires. We just had a substantial wildfire season here in Alaska, and those wildfires certainly contribute to additional permafrost thaw by sometimes removing that insulating layer of soil that might keep that ground frozen, as well as directly adding heat to the to the soil." "There are other changes that might be causing permafrost thaw, like anthropogenic changes, changes in land use patterns. As we build and develop roads into areas that haven't been touched by humans in a long time. We're seeing changes in disruption to permafrost." "Some people are quite interested in what might be coming out of the permafrost. We might see nutrients, as well as microorganisms that are moving from this frozen bank of soil into the active layer." "We're using next generation sequencing techniques to characterize not only who is in these soils, but also what they're doing." "I started as a faculty member in 2015. As I moved up to Alaska, I got some really great advice from a postdoctoral mentor that said, make sure you choose something local. I'm fortunate enough that I have access to permafrost thaw gradient, that's effectively in the backyard of my office." "Just a few miles from campus, we have access to a site that's managed by the Army Corps of Engineers. They have a cold regions group up here that runs a more famous permafrost tunnel. So they've dug a deep tunnel into the side of a hill that stretches back about 40,000 years into permafrost. They also have a great field site that has an artificially induced permafrost thaw gradient, and a majority of our published work has been generated by taking soil cores from that field site." "Maintaining that cold chain, whether it's experimental reagents or experimental samples, is a challenge for everyone. We're collecting active layer soil—the soil directly beneath our feet—so that's not at terribly extreme temperatures. But we do put it in coolers immediately upon extracting from the from the environment. Then we can bring it back to our lab where we can freeze it if we're going to use it for later analysis, or we can keep it at appropriately cool temperatures, if we're going to be working with the microbial community directly." "We were most interested in looking for microbes that might have impacts on the above ground. ecosystem. So when we were characterizing the microbial community, we were doing that because we also wanted to link it to above ground changes." "Changes in vegetation that might be driven by changes in microorganisms would certainly have an impact on the wildlife that are that are present at the site. So, just as an example, if we see a decrease in berries that might be present, that might decrease the interest from animals that rely on that [food source]. And so we might see changes in who's there." "Outside of my research, we've seen changes in the types of plants present across northern latitudes. So different willows, for instance, a

Dr. Marie Landry, Professor of Laboratory medicine and Infectious Diseases at Yale University School of Medicine and Dr. John Booss, former National Director of Neurology for the Department of Veteran's Affairs discuss the past, present and future of diagnostic virology. These proclaimed coauthors walk us through the impact of some of the most significant pathogens of our time in preparation for the launch of their 2nd edition of "To Catch a Virus," a book that recounts the history of viral epidemics from the late 1800s to present in a gripping storytelling fashion. Ashley's Biggest Takeaways Coauthoring a book requires having great respect for the opinions of the person you are working with. The first human disease shown to be viral in nature was yellow fever, but for quite some time, the mode of disease transmission remained mysterious. In early 1881, Carlos Finlay of Cuba suggested that the disease could be spread by mosquitoes and significantly advanced the field. It wasn't until polio was discovered in the early 1900s that scientists determined that viruses could also be transmitted by and animals. The ability to grow virus in tissue culture was another huge advancement in the field of diagnostic virology, which eventually led to the development of the Salk inactivated polio vaccine (IPV). Although he did not seek the spotlight for his work, Walter Roe, was a bright, hardworking (and one of John's favorite) virologist, who made important advances in tissue culture, researched the role of retroviruses in animal cancer and discovered adenoviruses. As a result of the COVID-19 pandemic, the clinical laboratory played a central role in public health. The importance of a laboratory diagnosis became more evident and next generation sequencing moved further into the clinical lab. Featured Quotes: "Advice that was given to me way back when I started on my first book is that you have to write about something you're passionate about. You have to really believe in the topic because otherwise it'll come across as superficial and artificial. So the very first step is do you really believe in, [and in the case of writing a book, that means] believe in what you're writing about." – Booss. "Science is often projected as a steady stream of advances one after the other. But there is a certain amount, I think, of arbitrary choice at each step. And it's also true for for writing a book." – Booss "In putting the book together, there are obviously major events that occurred in virology, major crises that move the field forward, an interplay, really, of the scientific advances, the clinical need of the crisis at hand and some very remarkable people. One highlight of this book is the way it does focus on individuals and their stories and how they contributed to that progress." -Landry "When [pathogens] spread from a local area to a larger area geopolitical area or even globally, they become pandemic." Polio "The most compelling virus that I can think of in my youth was obviously polio. So when I was a small child, polio was causing epidemics every summer, at the end of which, between 20 and 30,000 children in the United States were left either paralyzed or dead. So this was it really struck fear into parents hearts." – Landry "And then came the oral polio vaccine. We lined up, and it was a very, very painless way to be immunized. So that was a tremendous success story, we've come very close to eliminating polio, because of a number of reasons it hasn't happened." - Landry "There was a case recently of paralytic polio in New York, in an unvaccinated person. And I hope this is a wake-up call, we really thought we were about to eliminate before COVID. And then with those disruptions and others, there's been a little resurgence, but I hope that it will be accomplished soon." -Landry COVID-19 "It's amazing how much the world did change. International economies collapsed. whole societies shut down. The education and socialization of children came to a screeching halt. As schools close, whole chasms of inequality opened up or were revealed. And also the poor and marginalized people were the ones who suffered most. And the U.S. cultural divisions interfered with attempts to block the disease. So that by 2022, the U.S. was unique in having over 1 million deaths. We lead unfortunately led the world in that regard." – Booss "Sometimes we need a crisis to move us forward. And we saw this with the new vaccine platforms, especially the mRNA vaccine." Let us know what you thought about this episode by tweeting at us @ASMicrobiology or leaving a comment on facebook.com/asmfan. Links From yellow fever and smallpox, to polio, AIDS and COVID-19, To Catch a Virus guides readers through the mysterious process of catching novel viruses and controlling deadly viral epidemics— and the detective work of those determined to identify the culprits and treat the infected. The new edition will be released October 15, 2022, available at asm.org/books

Dr. Wun-Ju Shieh, worked as a pathologist and infectious diseases expert with the CDC from 1995-2020. He recounts his experiences conducting high risk autopsies on the frontlines of outbreaks including Ebola, H1N1 influenza, monkeypox and SARS-CoV-1 and 2. He also addresses key questions about factors contributing to the (re)emergence and spread of pathogens and discusses whether outbreaks are becoming more frequent or simply more widely publicized. Ashley's Biggest Takeaways: • Pathologists are a group of medical doctors serving behind the line of the daily hospital activities. • Pathology service can be divided into atomic pathology and clinical pathology. The field covers all the laboratory diagnostic work in the hospital, and clinical microbiology or medical microbiology is actually a subdivision within the clinical pathology service. • Usually, a pathologist working in a hospital will examine and dissect tissue specimens from surgery or biopsy. • The pathologist also performs autopsies as requested to determine or confirm the cause of death. • Serving as first a clinician in Taiwan and then a pathologist in the United States has provided Shieh with the unique experience of evaluating patients from both the outside-in and the inside-out! • Even when a major outbreak of a known etiologic agent is taking place, confirmatory diagnosis is necessary for subsequent quarantine, control and prevention of the outbreak. • During major disease outbreaks, other pathogens do not go away, and we must simultaneously facilitate their timely diagnosis to ensure effective patient treatment and care. • SARS-CoV-2 appears to be transmitted more easily than SARS-CoV-1. One possible explanation for this is that the amount of viral load appears to be the highest in the upper respiratory tract of those with COVID-19, shortly after the symptoms develop. This indicates that people with COVID-19 may be transmitting the virus early in infection, just as their symptoms are developing…or even before they appear or without symptoms. • SARS-CoV-1 viral loads peak much later in the illness. • Asymptomatic transmission is rarely seen with SARS-CoV-1 infection. • Almost 99% of SARS-CoV-1 patients developed prominent fever when they started to carry infectivity. Temperature monitoring was therefore, very effective at detecting sick patients and facilitating prompt quarantining procedures, which effectively contained/minimized transmission of the virus. • This was not as effective for SARS-CoV-2, despite early attempts at temperature. monitoring. • SARS-CoV-2 was much harder to contain both because of the milder display of host symptoms and the demonstration of higher viral transmissibility.

Dr. Linden Hu, Vice Dean for Research at Tufts University in Boston Massachusetts and Paul and Elaine Chervinsky Professor in Immunology, discusses new and ongoing research pertaining to the prevention, treatment and diagnosis of human Lyme disease. He also discusses some of the key unanswered questions about Lyme, such as how B. burgdorferi adapts to different hosts and environments and why some patients have been known to exhibit persistent symptoms even after treatment. Links mentioned: Webinar - Vector-Borne Disease in a Changing Climate https://asm.org/Webinars/Vector-Borne-Disease-in-a-Changing-Climate The Bulls-Eye Rash of Lyme Disease: https://asm.org/Articles/2018/April/going-skin-deep-investigating-the-cutaneous-host-p Pfizer and Valneva Initiate Phase 3 Study of Lyme Disease Vaccine Candidate VLA15 https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-valneva-initiate-phase-3-study-lyme-disease Could This Treatment Prevent Chronic Lyme Disease? https://news.northeastern.edu/2021/10/06/preventing-chronic-lyme-disease/ Promising New Drug Would Eradicate Lyme While Leaving Gut Microbes Alone: https://www.lymedisease.org/members/lyme-times/2022-spring-news/targeted-lyme-disease-drug/ A Tick's Meal: https://asm.org/Podcasts/TWiM/Episodes/A-Tick-s-Meal-TWiM-258 Evidence That the Variable Regions of the Central Domain of VlsE Are Antigenic during Infection with Lyme Disease Spirochetes https://journals.asm.org/doi/10.1128/IAI.70.8.4196-4203.2002 Distinct Roles for MyD88 and Toll-Like Receptors 2, 5, and 9 in Phagocytosis of Borrelia burgdorferi and Cytokine Induction https://journals.asm.org/doi/10.1128/IAI.01600-07

Dr. Mark O. Martin, Associate professor of biology at the University of Puget Sound in Tacoma, Washington is a distinguished educator with a well-known social media presence. He discusses how he became interested in microbiology and what drives his varied research foci, including #Microbialcentricity, bacterial predation, bioluminescence, tardigrades, microbial midwives and more. In the process, he delves into his passion for using art and other creative approaches to facilitate learning in the classroom, and shares some experience-driven wisdom about building confidence in STEM. Links for this Episode: Vertically transmitted microbiome protects eggs from fungal infection and egg failure https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-021-00104-5 The effects of Sceloporus virgatus cloacal microbiota on the growth of pathogenic fungi https://soundideas.pugetsound.edu/summer_research/426/ Sex-specific asymmetry within the cloacal microbiota of the striped plateau lizard, Sceloporus virgatus https://link.springer.com/article/10.1007/s13199-010-0078-y Predatory Prokaryotes: An Emerging Research Opportunity (pdf) https://www.pugetsound.edu/sites/default/files/file/martin2002_0.pdf Carleton College #LuxArt 2019 https://www.youtube.com/watch?v=fztiJ3o7uWs

Dr. Elizabeth Dinsdale, Matthew Flinders Fellow in Marine Biology in the College of Science and Engineering at Flinders University in Adelaide, Australia, uses genomic techniques to investigate the biodiversity of microbial communities in distinct ecological niches, including coral reefs, kelp forest and shark epidermis. She discusses how shotgun metagenomics is being used to characterize the architecture of microbial communities living in the thin layer of underlying mucus on shark's skin, and how understanding the function of these microbes is providing clues to important host-microbe interactions, including heavy metal tolerance. Ashley's Biggest Takeaways: Sharks belong to a subclass of cartilaginous fish called elasmobranchs and are unique in that their epidermises are covered in dermal denticles—overlapping tooth-like structures that reduce drag and turbulence, helping the shark to move quickly and quietly through the water. These dermal denticles are sharp (if you're going to pet a shark, make sure you go from the head to the tail to avoid getting cut!), and depending on the species of shark, may be more or less spread out across the epidermis. Where do microbes enter the story? Dermal denticles overlay a thin layer of mucus, which provides a distinctive environment for microbial life. Collecting microbial samples from underneath a shark's dermal denticles is quite difficult, and the technique varies by shark species (shark size, water depth and ability to bite all factor into the equation). Liz's team uses a specially designed tool that the group affectionately calls a "supersucker," to create and capture a slurry of microbes and water for analysis. The team then uses shotgun metagenomics to identify and characterize the microbes in their collected samples. Sequencing has revealed biogeographical difference, as well as similarities in microbial architecture of whale sharks across the globe. There are 2 populations of whale sharks—one in the Atlantic Ocean and the other in the Indian Pacific Ocean. Samples collected from both populations have revealed that each individual whale shark, from within each aggregation, shares many of the same microbes. In fact, unlike algae which may share 1 to 2 microbial species, whale sharks share about 80% of microbes across every individual. Since many of the sharks don't cross aggregations, Liz's team is investigating the possibility of coevolution between microbes and hosts. Metagenomic sequencing also provides information about the function of the sequenced microbes. High presence of heavy metal-tolerant microbes has been found in the epidermis of all shark species that the team has analyzed. Sharks are known to carry high levels of heavy metals in their skin, muscle and even blood. However, muscle tissue samples contain lower concentrations than skin, indicating that there may be a density gradient in place, and raising questions about how microbes might be involved in this regulation. Is there a pathway by which the microbes metabolize and help to remove concentrations of heavy metals across the epidermis? Liz and her team are hoping to find out. Links: Elizabeth Dinsdale https://www.flinders.edu.au/people/elizabeth.dinsdale Tracking Pathogens via Next Generation Sequencing (NGS) https://asm.org/Magazine/2021/Spring/Tracking-Pathogens-via-Next-Generation-Sequencing Microbial Ecology of Four Coral Atolls in the Northern Line Islands https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001584 Coral Research https://coralandphage.org/research_coral.php Metagenomic analysis of stressed coral holobionts https://pubmed.ncbi.nlm.nih.gov/19397678/ Metagenomic analysis of the microbial community associated with the coral Porites astreoides https://pubmed.ncbi.nlm.nih.gov/17922755/

Dr. Mallory Choudoir, microbial ecologist and evolutionary biologist at the University of Massachusetts Amherst shares how she leverages microbial culture collections to infer ecological and evolutionary responses to warming soil temperatures. She discusses complexities of the soil microbiome and microbial dispersal dynamics, and introduces fundamental concepts about the intersection between microbes and social equity. Ashley's Biggest Takeaways: Microbial culture collections are fundamental resources, serving as libraries where diverse species of microbes are identified, characterized and preserved in pure, viable form. Culture collections ensure conservation of species diversity and sustainable use of the collected microbes. For soil microbiologists, like Mallory Choudoir, culture collections provide the opportunity to connect patterns of genomic variation and microbial physiology to the conditions under which a particular microbe was isolated. Soil is a complex environment from the perspective of a microbe. In order to coexist in such a biologically diverse environment, which consists of spatial heterogeneity, as well as heterogeneity in access to moisture and nutrients, microbes must evolve different strategies to survive as part of a stable community. Choudoir's field site is based in the Harvard Forest Long Term Ecological Research Program's field site, where coils are buried and have been heating the forest soil to 5 degrees above ambient temperatures for nearly 30 years. The study allows Choudoir and colleagues to observe and evaluate long-term responses to chronic soil warming stress. This research is important because microbes function as resources to the health and well-being of ourselves and our planet. Understanding how microbes adapt to biotic and abiotic stresses can help inform future conservation strategies, biotechnological approaches and applications and equitable allocation of microbial resources. Visit https://asm.org/mtm for links mentioned

Peter Hotez talks about the global impact and historical context of neglected tropical diseases. He also highlights important developments in mass drug administration and vaccine research and shares why he chose to publish the third edition of Forgotten People, Forgotten Diseases during the COVID-19 pandemic. Ashley's Biggest Takeaways Neglected Tropical Diseases (NTDs) are chronic and debilitating conditions that disproportionately impact people in low- and middle-income countries (LMICs). Many of these diseases are parasitic, such as hookworm infection, schistosomiasis and chagas disease; however, in recent years, several non-parasitic infections caused by bacteria, fungi and viruses, as well as a few conditions that are not infections, including snake bite and scabies (an ectoparasitic infestation), have been added to the original NTD framework (established in the early 2000s). What do most NTDs have in common? High prevalence. High mortality; low morbidity. Disabling. Interfere with people's ability to work productively. Impact child development and/or the health of girls and women. Occur in a setting of poverty and actually cause poverty because of chronic and debilitating effects. Hotez and his colleagues recognized that there is a uniqueness to the NTDs ecosystem, and they began putting together a package of medicines that could be given on a yearly or twice per year basis, using a strategy called Mass Drug Administration (MDA). This involved the identification of medicines that were being used on an annual basis in vertical control programs and combining those medications in a package of interventions that costs about $0.50 per person per year. "Throw in an extra 50 cents per person and we could double or triple the impact of public health interventions," he explained. Emerging diseases, such as SARS-CoV-2, capture the attention of the public for obvious reasons. They pose an imminent threat to mankind. NTDs are not emerging infections, but they are ancient afflictions that have plagued humankind for centuries and, as a consequence, have had a huge impact on ancient and modern history. One of the reasons we have mainland China and Taiwan today may have been, in part, due to a parasitic infection, Schistosomiasis. Hotez and colleagues at the Texas Children's Center for Vaccine Development have developed a COVID-19 vaccine, based on simple technology, similar to what is used for the Hepatitis B vaccine. They hope to release the vaccine for emergency use in resource poor countries like India and Indonesia. When asked about the timing of the publication of his book, the third edition of Forgotten People, Forgotten Diseases, Hotez acknowledged the difficulty of helping countries understand that NTDs have not gone away. COVID-19 is superimposed on top of them, and the pandemic has done a lot of damage in terms of NTD control. Although social disruption has interfered with the ability to deliver mass treatments, Hotez said that it has been gratifying to see that the USAID and their contractors have responded by putting out guidelines about how to deliver mass treatments with safe social distancing. "As a global society, we have to figure out how to walk and chew gum at the same time," he said. "We've got to take care of COVID, but we really must not lose the momentum we've had for NTDs because the prevalence is starting to decline and we're really starting to make an impact."

Rita Colwell has made major advances in basic and applied microbiology, largely focused on Vibrio cholerae. She describes several lines of evidence for the environmental niche of the bacterium, as well as her work to predict and prepare for cholera outbreaks. Colwell closes with her thoughts on why it's a great time to be a microbiologist.

Denise Akob discusses her studies of microbial communities of contaminated and pristine environments using life science and earth science techniques. She discusses how to figure out "who's there," how to optimize select natural microbial activities, and her career path into government research. Julie's Biggest Takeaways: Biogeomicrobiology straddles the life science and earth science fields. This is a growing area of research in the academic setting as well as in the private sector, where one can contribute to hydrogeology or bioremediation efforts. What happens on the surface when extracting resources like natural gases? Wastewater from hydraulic shale fracking, or fracking, can contaminate microbes. Preliminary data suggests that microbes that thrive in that wastewater can be a fingerprint for surface contamination, and this is one of the areas of active research in Akob's lab. Additionally, microbes can respond to contaminants to remove that risk and remediate the spills. One trip to the field can provide samples for years of analysis. From one sample, scientists can conduct: Microbiome studies through amplicon sequencing to understand population structures. Metagenomics studies to understand functional potential. Biochemical studies to understand active metabolic processes. Akob asks how to make natural microbial degraders happy. For example: acetylene, a triple-bonded carbon compound, can inhibit degradation of chlorinated solvents, a potent groundwater contaminant. By studying the microbes that use acetylene as a primary energy source (acetylenotrophs), this removes this inhibition caused by acetylene and the chlorinated solvent-degraders can increase their activity. Akob studies pristine environments to understand natural microbial communities. A cave she studied in Germany was 'ultra pristine,' discovered while building a highway. Understanding natural processes, such as the biomineralization promoted during stalagmite and stalactite formation helps scientists imagine how to use tehse processes in other applications. Links for this Episode: Mumford AC et al. Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities. Applied and Environmetnal Microbiology. 2018. Akob DM et al. Acetylenotrophy: a Hidden but Ubiquitous Microbial Metabolism? FEMS Microbial Ecology. 2018. Akob DM et al. Detection of Diazotrophy in the Acetylene-Fermenting Anaerobic Pelobacter sp. Strain SFB93. Applied and Environmental Microbiology. 2017. ASM Article: The Microbial World of Caves James J, Gunn AL, and Akob DM. Binning Singletons: Mentoring through Networking at ASM Microbe 2019. mSphere. 2020. HOM Tidbit: Scientists Find Ancient Cave Dwelling Resistant Bacteria ASM Press: Women in Microbiology

How does tick biology influence their ability to transmit disease? Marshall Bloom explains the role of the tick salivary glands in Powassan virus transmission and the experiments that led to this discovery. He also provides a historical background for the Rocky Mountain Labs in Hamilton, Montana, and talks about the 3 elements to consider when working with potentially harmful biological agents. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS or by email. Julie's Biggest Takeaways There are 3 elements to consider when working with potentially harmful biological agents: Biosafety: protecting the laboratory workers from the infectious agents in the lab. Biocontainment: protecting the community by keeping the infectious agent contained within the facility. Bioassurity: protecting the individual by ensuring those working with infectious agents are capable to do so. You need 4 bites of an APPLE for full lab safety, for work in labs from high school level through biosafety level 4: A: Administration. Training, paperwork, etc. P: Personal protective equipment (PPE). Varies from gloves to positive pressure suits, depending on the microorganisms under study. PL: Laboratory procedures. Standard operating protocols. E: Engineering. Biosafety cabinets and labs that have protective features. Most of the vector-borne flaviviruses, including Powassan virus, don't cause overt disease in the people they infect, so many people never know they've been infected. Without serological surveys, it's difficult to know the full range of infected individuals versus those that develop serious disease. Serious disease often manifests in neurological symptoms such as encephalitis, with 10-15% mortality rate; half of those suffering neurological disease will continue to have serious sequelae for years. The Rocky Mountain Labs was once the world reference center for ticks: it held thousands of samples which represented the type species for the entire world. The tick salivary glands look like a bunch of grapes: the stem of the grapes is a series of branching ducts. The "grapes" at the end of the ducts are the acini, which is Latin for 'little sac.' These acini play a major role in tick feeding, and different types of acini play different functional roles: Type 1 acini: cells have no granules. Acini involved with fluid exchange. Type 2 and type 3 acini: cells with granules. Cells degranulate to release vasoactive compounds into tick saliva during feeding. Featured Quotes "The first isolation of Powassan virus was from a little boy in Powassan, Canada in 1958. If you look at the cases over the years, the numbers are going up, but compared to Lyme disease, they're pretty low: there's been less than 200 cases, all told." "Amazingly, the Powassan virus can be transmitted in as little as 15 minutes….[and] a female tick can take days to get a full meal." "I take a tick-centric view. If I can anthropomorphize, as my old friend Stanley Falkow used to say, he'd say 'think like the microbe.' The microbe doesn't really care if we get sick or not. The microbe is just trying to make a living and survive." "One of the really surprising things is that infected ticks can infect uninfected ticks, if they are feeding right next to each other. Ticks like to feed in groups: it's called co-feeding. The virus can transferred really quickly, 15 min, which is way faster than the virus can go through a replication cycle. What that means to me is that the ticks are infecting each other….we want to investigate the role of co-feeding." "If something sounds like fun or sounds important, and especially if something sounds fun AND important, then you should do it." Links for this Episode: Paules CI et al. Tickborne Diseases--Confronting a Growing Threat. New England Journal of Medicine. August 2018. Amazon: Fighting Spotted Fever in the Rockies by Esther Gaskins Price New York Times: Kay Hagan obituary Grabowski JM et al. Dissecting Flavivirus Biology in Salivary Gland Cultures from Fed and Unfed Ixodes scapularis (Black-Legged Tick). mBio. January 2019. ASM on Instagram Grabowski JM, Offerdahl DK, and Bloom ME. The Use of Ex Vivo Organ Cultures in Tick-Borne Virus Research. ACS Infectious Disease. Marhc 2018. Twitter thread from @BugQuestions: Rocky Mountain Spotted Fever and Howard Ricketts History of Microbiology Tidbit: A Short History of the Screwworm Program

What kinds of microorganisms can degrade oil? How do scientists prioritize ecosystems for bioremediation after an oil spill? Joel Kostka discusses his research and the lessons from the Deepwater Horizon oil spill that will help scientists be better prepared for oil spills of the future. Links for this Episode: Joel Kostka Lab Website Kostka J. et al. Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Applied and Environmental Microbiology. 2011. Shin B. et al. Succession of Microbial Populations and Nitroget-Fixation Associated With the Biodegradation of Sediment-Oil-Agglomerates Buried in a Florida Sandy Beach. Scientific Reports. 2019. Bociu I. Decomposition of Sediment-Oil-Agglomerates in a Gulf of Mexico Sandy Beach. Scientific Reports. 2019. Overhold W.A. et al. Draft Genome Sequences for Oil-Degrading Bacterial Strains from Beach Sands Impacted by the Deepwater Horizon Oil Spill. Genome Announcements. 2013. Gulf of Mexico Research Initiative ASM Colloquia Report: Microbial Genomics of the Global Ocean System ASM Article: Microbiomes: An Origin Story Joyful Microbe Blog: How to make a Winogradsky column Small Things Considered: How to Build a Giant Winogradsky Column 20% off The Invisible ABCs for MTM listeners! Use promo code: ABC20 at checkout.

How do arboviruses evolve as they pass between different hosts? Greg Ebel discusses his research on West Nile virus evolution and what it means for viral diversity. He also talks about using mosquitos' most recent blood meal to survey human health in a process called xenosurveillance. Julie's Biggest Takeaways: Mosquitoes and other arthropods have limited means of immune defense against infection. One major defense mechanism is RNA interference (RNAi). RNAi uses pieces of the West Nile viral genome to select against the viral genome, which helps select for broadly diverse viral sequences. The more rare a viral genotype, the more likely it is to escape negative selection inside the mosquito host, allowing this viral sequence to increase in frequency. West Nile virus passes largely between birds and mosquitos. Culex mosquitos tend to prefer birds, and this leads to an enzootic cycle for the virus passing between birds and mosquitos. The viral life cycle inside the mosquito has several important steps: The virus first enters as part of the mosquito blood meal. The virus infects epithelial cells of the mosquito midgut. After 3-5 days, the virus leaves the midgut (midgut escape) to enter the mosquito hemolymph. In the next mosquito blood meal, virus is expelled with saliva, which has anticoagulant activity. West Nile virus selection undergoes cycles of selection as it passes from vertebrates (mostly birds) to invertebrates (mosquitos): In vertebrates, the virus must escape to cause viremia in a short period of time for replication to occur before the immune system recognizes and eliminates the virus. This leads to purifying selection, or elimination of amino acid variation that decreases viral protein function. In mosquitos, the virus spends several days in the midgut epithelial cells and then hemolymph, leading to a longer selection time. This leads to more viral diversity in the mosquito host. RNAi further drives population diversity. Through stochasticity, a single viral population will often come to dominate a single infected mosquito. How do scientists know which virus replicates best? Competitive fitness tests measure which virus grows to a higher population in a given environment. A manipulated virus (one passaged in a mosquito or selectively mutated at distinct sequences) and its non-manipulated parent sequence are inoculated at known proportions, and given a certain amount of time to replicate. By measuring the final proportions, Greg and his team can determine which sequence was more fit in that given environment. Xenosurveillance uses mosquitoes to detect a wide array of pathogens at clinically relevant levels. Testing began with in vitro blood-bag feeding, and was validated with studies in Liberia and Senegal. The microorganism sequences are so diverse that the information was used to identify novel human viruses. These studies also provide insight into mosquito feeding habits, which helps in disease modeling. Links for this Episode: Greg Ebel Lab Website Rückert C. et al. Small RNA Responses of Culex Mosquitoes and Cell Lines during Acute and Persistent Virus Infection. Insect Biochemistry and Molecular Biology. 2019. Grubaugh N.D. et al. Mosquitoes Transmit Unique West Nile Virus Populations during Each Feeding Episode. Cell Reports. 2017. Grubaugh N.D. and Ebel G.D. Dynamics of West Nile Virus Evolution in Mosquito Vectors. Current Opinion in Virology. 2016. Fauver J.R. et al. Xenosurveillance Reflects Traditional Sampling Techniques for the Identification of Human Pathogens: A Comparative Study in West Africa. PLoS Neglected Tropical Diseases. 2018. Fauver J.R. The Use of Xenosurveillance to Detect Human Bacteria, Parasites, and Viruses in Mosquito Bloodmeals. American Journal of Tropical Medicine and Hygiene. 2017. Tracey McNamera: Canaries in the Coal Mine TEDxUCLA New York Times: Encephalitis Outbreak Teaches an Old Lesson. 1999. ASM Article: The One Health of Animals, Humans, and Our Planet: It's All Microbially Connected

How can the intricate relationship between soil microbiota and plants be managed for improved plant health? Linda Kinkel discusses new insights into the plant rhizosphere and the ways that some Streptomyces isolates can protect agricultural crops against bacterial, fungal, oomycete, and nematode infections. Julie's Biggest Takeaways: The soil microbiome is extremely dynamic, with boom-and-bust cycles driven by nutrient fluxes, microbial interactions, plant-driven microbial interactions, and signaling interactions. Finding the source of these boom-and-bust cycles can help people to manage the microbiome communities and produce plant-beneficial communities for agricultural purposes. Rhizosphere soil is soil closely associated with the root and is distinct from rhizoplane soil that directly touches the root. The endophytic rhizosphere are those microbes that get inside the root. Many scientists view these communities as a continuum rather than sharply delineated. Plants provide necessary carbon for the largely heterotrophic soil microbiota, and these microorganisms help the plants in several ways too: Microbes mediate plant growth by production of plant growth hormones. Microbes provide nutrients through mechanisms like nitrogen fixation or phosphorus solubilization. Microbes protect the plant from stress or drought conditions. Through a University of Minnesota plant pathology program, potatos were passaged in a field for over 2 decades to study potato diseases. Over time, researchers found fewer diseases in test crops, which led the plot to be abandoned in the late 1970s. In the 1980s, Dr. Neil Anderson planted potatoes to see if they would develop disease, but neither Verticillium wilt nor potato scab developed among the plants. Soil from the field (and on the potatoes) contained Streptomyces isolates that showed antimicrobial activity against bacteria, fungi, nematodes, and oomycetes. This discovery led Neil, new University of Minnesota professor Linda, and their collaborators to study the antimicrobial activity of natural Streptomyces isolates from around the world. Inoculation quickly adds specific microbial lineages to soil microbiome communities. Alternatively, land can be managed by providing nutrients to encourage the growth of specific species, like Streptomyces, within a given plot, but this takes longer to develop. How are soil microbiomes inoculated? Microbes can be: Added to the seed coating before planting. Placed in the furrow when the seed is planted. Distributed into the irrigation system. Links for this Episode: Linda Kinkel website at University of Minnesota Essarioui A. et al. Inhibitory and Nutrient Use Phenotypes Among Coexisting Fusarium and Streptomyces Populations Suggest Local Coevolutionary Interactions in Soil. Environmental Microbiology. 2020. Schlatter D.C. et al. Inhibitory Interaction Networks Among Coevolved Streptomyces Populations from Prairie Soils. PLoS One. 2019. Schlatter D.C. et al. Resource Use of Soilborne Streptomyces Varies with Location, Phylogeny, and Nitrogen Amendment. Microbial Ecology. 2013. Small Things Considered blog: Are Oomycetes Fungi or What? International Year of Plant Health HOM Tidbit: Austin-Bourke P.M. Emergence of Potato Blight, 1843-1846. Nature. 1965.

Pathogenic E. coli are different than lab-grown or commensal E. coli found in the gut microbiome. Alfredo Torres describes the difference between these, the method his lab is using the develop vaccines against pathogenic E. coli, and how this same method can be used to develop vaccines against Burkholderia infections. Julie's Biggest Takeaways: coli plays many roles inside and outside the scientific laboratory: Laboratory E. coli strains used by scientists to study molecular biology. Commensal E. coli strains contribute to digestion and health as part of the intestinal microbiome. Pathogenic E. coli strains have acquired factors that allow them to cause disease in people The pathogenic E. coli associated with diarrheal disease are the ones named for their O-antigen and flagellar H-antigen, such as O157:H7. There are about 30 E. coli strains with various combinations of O-H factors known to cause diarrheal disease in people. The E. coli Shiga toxin (though not the bacterium itself) can pass through the epithelial cell layer to become systemic, and eventually the toxin will accumulate in the kidneys. This can lead to patients experiencing hemolytic uremic syndrome (HUS) and kidney failure, leading to lifelong dialysis or need for a transplant. An immune response that prevents the E. coli from attaching will prevent the bacterium from secreting toxin in close proximity to the epithelial cells and decrease likelihood of HUS development. Burkholderia is a bacterial genus whose member species have been weaponized in the past, and which remain potent disease-causing agents around the world. B. mallei causes glanders, a disease mostly of horses and their handlers. It is a respiratory infection that can become systemic if not treated. B. pseudomallei causes melioidosis, a disease that can manifest in many ways. It is endemic in many tropical regions around the world, found in over 79 countries so far. Coating gold nanoparticles with antigens against which the immune response will be protective is a method Alfredo has used for a number of candidate vaccines, including one against E. coli and one against B. pseudomallei. The nanoparticles can have the gold cleaved off to provide different functional variants of the same vaccine. Links for this Episode: Alfredo Torres webpage at University of Texas Medical Branch McWilliams BD and Torres AG. Enterohemorrhagic Escherichia coli Adhesins. Microbiology Spectrum. 2013. Sanchez-Villamil JI et al. Development of a Gold Nanoparticle Vaccine against Enterohemorrhagic Escherichia coli O157:H7. mBio. 2019. Wiersinga WJ et al. Melioidosis. Nature Reviews Disease Primers. 2018. Khakhum N. et al. Evaluation of Burkholderia mallei ΔtonB Δhcp1 (CLH001) as a live attenuated vaccine in murine models of glanders and melioidosis. PLOS Neglected Tropical Diseases. 2019. Torres AG. Common Sense Can Keep You Safe in E. coli Outbreak. Galveston County Daily News. 2020. ABRCMS: Annual Biomedical Research Conference for Minority Students MTM: Burkholderia pseudomallei & the neglected tropical disease melioidosis with Direk Limmathurotsakul HOM Tidbit: Kiyoshi Shiga Biography in Clinical Infectious Diseases

Does the fetus have a microbiome? How does the placenta prevent infection? Carolyn Coyne talks about placental structure and biology, and why studying the maternal-fetal interface remains a critical area of research. Julie's Biggest Takeaways: The placenta forms within 3-5 days post conception as a single layer of cells surrounding the fertilized embryo. These cells differentiate and develop into more complex structures. Very few microbes cause fetal disease. Of those that do, the disease-causing microorganisms are diverse and can lead to serious congenital defects or even death of a developing fetus. These microbes are largely grouped into the TORCH (now TORCH-Z) microorganisms: Toxoplasma gondii Other (a variety of different bacteria and viruses) Rubella Cytomegalovirus Herpesviruses Zika virus The fetus is immunologically immature and unable to protect itself. Some of the maternal immunological molecules (such as maternal antibodies) cross the placenta to protect the fetus, but that only happens during later stages of fetal development. Between the first and second trimesters, the maternal vasculature reorganizes and maternal antibodies can begin to reach the fetus. This increases over time, until the end of the third trimester, when there is a higher concentration of maternal antibodies in fetal blood than in maternal blood. In the later stages of development, the placenta is coated in a layer of fused cells, leading to a shared cytoplasm that covers the entire surface area of the placenta. This fused-cell layer is formed from syncytiotrophoblasts, and the fusion is facilitated by the activity of an endogenous retrovirus fusion protein. Syncytiotrophoblasts are extremely resistant to infection with a number of different pathogens, and pathogen types. In initial tests experiments, Carolyn and her research team discovered that these cells releasing certain antimicrobial molecules to share protective properties. Syncytiotrophoblasts secrete type III interferons, which play a big role at barrier surfaces such as the airway and the gut—but unlike these barriers, the syncytiotrophoblast cells secrete type III interferons constitutively. Links for this Episode: Carolyn Coyne Website on the University of Pittsburgh School of Medicine Arora N. et al. Microbial Vertical Transmission during Human Pregnancy. Cell Host & Microbe. May 2017. Coyne C.B. The Tree(s) of Life: The Human Placenta and My Journey to Learn More About It. PLoS Pathogens. April 2016. Ander S.E. et al. Human Placental Syncytiotrophoblasts Restrict Toxoplasma gondii Attachment and Replication and Respond to Infection by Producing Immunomodulatory Chemokines. mBio. January 2018. Wells A.I. and Coyne C.B. Type III Interferons in Antiviral Defenses at Barrier Surfaces. Trends in Immunology. October 2018. Ander S.E. Diamond M.S. and Coyne C.B. Immune Responses at the Materna-Fetal Interface. Science Immunology. January 2019. HOM Tidbit: Women in Microbiology HOM Tidbit: Small Things Considered blog post: Retroviruses, the Placenta, and the Genomic Junk Drawer

Are there drugs that can treat coronaviruses? Timothy Sheahan talks about his drug discovery work on a compound that can inhibit all coronaviruses tested so far, and tells how his career path took him to pharmaceutical antiviral research and then back to academia. Julie's Biggest Takeaways: Even though the MERS-CoV was discovered as a human pathogen in 2012, it was likely percolating as a disease agent for a long time before that. Banked camel serum provides evidence that the virus had been circulating in camels for several decades prior. Differentiated ex vivo lung cultures allow study of virus infection in a 3D model representation for studying viral infection, including target cell types of both MERS-CoV and SARS-CoV. SARS-CoV prefers ciliated epithelial cells Ace2 MERS-CoV prefers nonciliated epithelial cells DPP4 Coronavirus disease in people takes place over a course of about 2 weeks. In mice, the disease is similar, but progression is faster, taking about 1 week. The drug remdesivir (RDV) is a nucleoside analog that inhibits the coronavirus RNA-dependent RNA polymerase (RDRP). Remdesivir activity has not been tested against nCoV2019, but similarity to other viruses is promising. Bioinformatic approaches show that the nCoV2019 RDRP is 99% similar and 96% identical to SARS-CoV RDRP. Remdesivir works against every coronavirus tested so far, including viruses with highly divergent RDRP sequences, so remdesivir is likely to be effective again nCoV2019. Experiments must still be performed before reaching this conclusion, of course. Tim also hopes to discover the genetic determinants that will allow a chronic hepatitis C virus (HCV) infection in mice, but not standard inbred mice. He uses outbred mice meant to mimic the diversity of the human population, and strengthen the results. Understanding these determinants would inform human studies to better understand chronic HCV infection. Links for this Episode: MTM Listener Survey, only takes 3 minutes. Thanks! TWiV 584: Year of the Coronavirus Timothy Sheahan website at University of North Carolina Sheahan T.P. et al. Broad-Spectrum Antiviral GS-5734 Inhibits both Epidemic and Zoonotic Coronaviruses. Science Tranlational Medicine. 2017. Sheahan T.P. et al. Comparative Therapeutic Efficacy of Remdesivir and Combination Lopinavir, Ritonavir, and Interferon Beta against MERS-CoV. Nature Communications. 2020. Agostini M.L. et al. Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease. mBio. 2018. ASM Coronavirus Resource Page HOM Tidbit: Baltimore D. In Vitro Synthesis of Viral RNA by the Poliovirus RNA Polymerase. PNAS. 1964.